Error compiling program on Snow Leopard for 64 bit

cstrato · April 27, 2010, 9:24pm

Dear ROOTers

On my MacBook Pro I have just installed Snow Leopard and the new Xcode 3.2.2 from Apple.

First I have compiled root_v5.24/00 for 32 bit and tried to compile my program but got a link error. Since my Makefile
does “include Makefile.arch” from the root/test directory I downloaded the newest Makefile.arch from svn, which finally
allowed me to compile my program.

Then I have compiled root_v5.24/00 for 64 bit and tried to compile my program again, but this time I got this link error:

ld: invalid option to -undefined [ warning | error | suppress | dynamic_lookup ]
collect2: ld returned 1 exit status

Do you know the reason for getting this error?
Could there be a problem in the newest version of Makefile.arch?

BTW, in my “.bashrc” file I have:

export MACOSX_DEPLOYMENT_TARGET=10.6
#export MACOSX_DEPLOYMENT_TARGET=10.5
export ROOTSYS=/Volumes/CoreData/ROOT/root
export PATH=$ROOTSYS/bin:$PATH
export LD_LIBRARY_PATH=$ROOTSYS/lib:$LD_LIBRARY_PATH
export DYLD_LIBRARY_PATH=$ROOTSYS/lib:$DYLD_LIBRARY_PATH

Is this still correct for Snow Leopard?
Could this cause the problem?

Best regards
Christian

rdm · April 30, 2010, 9:51am

Hi,

what option did you specify to -undefined as ld complains about? The opt for 10.6 should be dynamic_lookup. Please check your Makefile carefully.

Cheers, Fons.

cstrato · April 30, 2010, 9:01pm

Dear Fons,

As I have already mentioned my Makefile does “include Makefile.arch” from the root/test directory, thus is uses “$(UNDEFOPT)”.
Now I realized that “macosx” and “macosxxlc” define UNDEFOPT, while “macosx64” and “macosxicc” do not. Thus I have changed it to:

ifeq ($(ARCH),macosx64)
# MacOS X >= 10.4 with gcc 64 bit mode (GNU gcc 4.*)
# Only specific option (-m64) comes from root-config
MACOSX_MINOR := $(shell sw_vers | sed -n 's/ProductVersion://p' | cut -d . -f 2)
ifeq ($(MACOSX_DEPLOYMENT_TARGET),)
MACOSXTARGET := MACOSX_DEPLOYMENT_TARGET=10.$(MACOSX_MINOR)
else
MACOSXTARGET := MACOSX_DEPLOYMENT_TARGET=$(MACOSX_DEPLOYMENT_TARGET)
endif
CXX           = g++
CXXFLAGS      = $(OPT2) -pipe -Wall -W -Woverloaded-virtual
LD            = $(MACOSXTARGET) g++
LDFLAGS       = $(OPT2)
UNDEFOPT      = dynamic_lookup
# The SOFLAGS will be used to create the .dylib,
# the .so will be created separately
ifeq ($(subst $(MACOSX_MINOR),,1234),1234)
DllSuf        = so
else
DllSuf        = dylib
endif
SOFLAGS       = -dynamiclib -single_module -undefined $(UNDEFOPT) -install_name $(CURDIR)/
endif

This did solve my problem, nevertheless I would appreciate if you would make the corresponding changes in “Makefile.arch” so that
people using this file do not experience this problem.

However, now I have another problem: While compilation works fine as standalone library, you may know that I have created an
R/Bioconductor package “xps” where the compilation is done from within R. Although the compilation works fine, it seems that
the compiled library “xps.so” cannot be loaded into R. I get the following error:

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so':
  dlopen(/Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so, 6): Symbol not found: __ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc
  Referenced from: /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so
  Expected in: flat namespace
 in /Volumes/CoreData/CRAN/xps.Rcheck/xps/libs/x86_64/xps.so
ERROR: loading failed

While I will ask the SIG-Mac mailing list what this error means, my question here is:
What does “__ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc” mean?
Do you have any hint why “__ZN10TCanvasImp11ShowMembersER16TMemberInspectorPc” is not found?

Best regards
Christian

cstrato · May 2, 2010, 7:55pm

Dear Fons,

Meanwhile I did some extensive testing on both Leopard and Snow Leopard using the attached Makefiles:

Makefile.txt: this is the Makefile of my program which does “include Makefile.arch”
Makefile_old.arch.txt: this is the old Makefile.arch which I use since a couple of years w/o problem
Makefile_new.arch.txt: this is the Makefile.arch from root_v5.27/02 where I have added $(UNDEFOPT)

1, Test on Leopard using Makefile_old.arch.txt:

I did the test using root_v5.24/00 and using root_v5.27/02 with both “./configure macosx” and “./configure macosx64”,
and in all cases everything worked fine. I could compile “xps.so” and run it from within root as expected, see e.g.:

ROOT 5.27/02 (trunk@33229, Apr 27 2010, 11:38:29 on macosx64)

CINT/ROOT C/C++ Interpreter version 5.17.00, Dec 21, 2008
Type ? for help. Commands must be C++ statements.
Enclose multiple statements between { }.
root [0] .L macro4XPSLeopard.C
root [1] Init("/Users/rabbitus/ROOT/rootcode/xps-x.x.x/src/xps.so")
root [2] RMATest3("tmp_Test3_rma","/Users/rabbitus/ROOT/rootdata/test")
Creating new temporary file </Users/rabbitus/ROOT/rootdata/test/tmp_Test3_rma.root>...

2, Test on Leopard using Makefile_new.arch.txt:

With “./configure macosx” I could compile my program but get the following runtime error:

ROOT 5.27/02 (trunk@33229, Apr 27 2010, 11:38:29 on macosx)

CINT/ROOT C/C++ Interpreter version 5.17.00, Dec 21, 2008
Type ? for help. Commands must be C++ statements.
Enclose multiple statements between { }.
root [0] .L macro4XPSLeopard.C
root [1] Init("/Users/rabbitus/ROOT/rootcode/xps-x.x.x/src/xps.so")
root [2] RMATest3("tmp_Test3_rma","/Users/rabbitus/ROOT/rootdata/test")
dyld: lazy symbol binding failed: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Users/rabbitus/ROOT/rootcode/xps-x.x.x/src/xps.so
  Expected in: dynamic lookup

dyld: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Users/rabbitus/ROOT/rootcode/xps-x.x.x/src/xps.so
  Expected in: dynamic lookup

However, with “./configure macosx64” I get the following compilation problem:

g++ -dynamiclib -single_module -undefined dynamic_lookup -install_name /Users/rabbitus/ROOT/rootcode/xps-x.x.x/src/ TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/Users/rabbitus/ROOT/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -lGui -pthread -Wl,-rpath,/Users/rabbitus/ROOT/root/lib -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so 
ld warning: in TMLMath.o, file is not of required architecture
ld warning: in TStat.o, file is not of required architecture
ld warning: in StatUtils.o, file is not of required architecture
ld warning: in XPSBase.o, file is not of required architecture
ld warning: in XPSUtils.o, file is not of required architecture
ld warning: in XPSSchemes.o, file is not of required architecture
ld warning: in XPSDataTypes.o, file is not of required architecture
ld warning: in XPSProjectHandler.o, file is not of required architecture
ld warning: in XPSData.o, file is not of required architecture
ld warning: in XPSProcessing.o, file is not of required architecture
ld warning: in XPSHybridizer.o, file is not of required architecture
ld warning: in XPSSelector.o, file is not of required architecture
ld warning: in XPSNormalizer.o, file is not of required architecture
ld warning: in XPSPreProcessing.o, file is not of required architecture
ld warning: in XPSNormation.o, file is not of required architecture
ld warning: in XPSFilter.o, file is not of required architecture
ld warning: in XPSAnalyzer.o, file is not of required architecture
ld warning: in XPSAnalysis.o, file is not of required architecture
ld warning: in rwrapper.o, file is not of required architecture
ld warning: in xpsDict.o, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libCore.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libCint.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libRIO.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libNet.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libHist.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libGraf.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libGraf3d.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libGpad.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libTree.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libRint.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libPostscript.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libMatrix.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libPhysics.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libMathCore.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libThread.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libfreetype.a, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libGui.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libGed.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libTreePlayer.so, file is not of required architecture
ld warning: in /Users/rabbitus/ROOT/root/lib/libTreeViewer.so, file is not of required architecture
g++ -bundle -undefined dynamic_lookup -O2 -m64 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o \
                   -o  xps.so

3, Test on Snow Leopard using Makefile_old.arch.txt:

With “./configure macosx” I get the following compilation error:

c++ -dynamiclib -single_module -undefined suppress TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/Volumes/CoreData/ROOT/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -lGui -pthread -Wl,-rpath,/Volumes/CoreData/ROOT/root/lib -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.dylib 
ld: can't use -undefined warning or suppress with -twolevel_namespace
collect2: ld returned 1 exit status
make: *** [xps.dylib] Error 1

In contrast, with “./configure macosx64” I can compile my program but get the following runtime error:

ROOT 5.27/02 (trunk@33229, Apr 27 2010, 11:38:29 on macosx64)

CINT/ROOT C/C++ Interpreter version 5.17.00, Dec 21, 2008
Type ? for help. Commands must be C++ statements.
Enclose multiple statements between { }.
root [0] .L macro4XPS.C
root [1] Init("/Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so")
root [2] RMATest3("tmp_Test3_rma","/Volumes/CoreData/ROOT/rootdata/testAB/xps-1.x.x")
dyld: lazy symbol binding failed: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so
  Expected in: flat namespace

dyld: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so
  Expected in: flat namespace

4, Test on Snow Leopard using Makefile_new.arch.txt:

With “./configure macosx” I get the following compilation problem:

g++ -dynamiclib -single_module -undefined dynamic_lookup -install_name /Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/ TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/Volumes/CoreData/ROOT/root/lib -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -lfreetype -lGui -pthread -Wl,-rpath,/Volumes/CoreData/ROOT/root/lib -lm -ldl  -lRIO -lGed -lTreePlayer -lTreeViewer -o  xps.so 
ld: warning: in TMLMath.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in TStat.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in StatUtils.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSBase.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSUtils.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSSchemes.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSDataTypes.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSProjectHandler.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSData.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSProcessing.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSHybridizer.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSSelector.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSNormalizer.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSPreProcessing.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSNormation.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSFilter.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSAnalyzer.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in XPSAnalysis.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in rwrapper.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in xpsDict.o, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libCore.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libCint.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libRIO.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libNet.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libHist.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libGraf.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libGraf3d.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libGpad.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libTree.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libRint.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libPostscript.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libMatrix.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libPhysics.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libMathCore.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libThread.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libfreetype.a, file was built for unsupported file format which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libGui.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libGed.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libTreePlayer.so, file was built for i386 which is not the architecture being linked (x86_64)
ld: warning: in /Volumes/CoreData/ROOT/root/lib/libTreeViewer.so, file was built for i386 which is not the architecture being linked (x86_64)
g++ -bundle -undefined dynamic_lookup -O2 -m32 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o \
                   -o  xps.so

In contrast, with “./configure macosx64” I can compile my program but get the following runtime error:

ROOT 5.27/02 (trunk@33229, Apr 27 2010, 11:38:29 on macosx64)

CINT/ROOT C/C++ Interpreter version 5.17.00, Dec 21, 2008
Type ? for help. Commands must be C++ statements.
Enclose multiple statements between { }.
root [0] .L macro4XPS.C
root [1] Init("/Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so")
root [2] RMATest3("tmp_Test3_rma","/Volumes/CoreData/ROOT/rootdata/testAB/xps-1.x.x")
dyld: lazy symbol binding failed: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so
  Expected in: flat namespace

dyld: Symbol not found: __ZN5TTree14SetMaxTreeSizeEx
  Referenced from: /Volumes/CoreData/ROOT/rootcode/xps-x.x.x/src_splice/xps.so
  Expected in: flat namespace

In summary, while “Makefile_old.arch.txt” does work on Tiger and Leopard but not on Snow Leopard, the new “Makefile_new.arch.txt”
does not work on Leopard nor on Snow Leopard.

Can you tell me what I need to change to get “Makefile_old.arch.txt” to work on Snow Leopard, too?

Why does “Makefile_new.arch.txt” not work?

Best regards
Christian
Makefile.txt (3.48 KB)
Makefile_old.arch.txt (12.4 KB)
Makefile_new.arch.txt (12.9 KB)

rdm · May 12, 2010, 11:10am

Hi Christian,

you need to use the current Makefile.arch for all platforms, the old one does not support 10.6 as it only checks for versions up to 10.5. Now a number of errors are due to mixing 32 and 64 bit versions at link time:

ld: warning: in XPSData.o, file was built for i386 which is not the architecture being linked (x86_64)

Make sure you set the right ROOTSYS, PATH and DYLD_LIBRARY_PATH when building your program. You can use:

or

to switch.

Next make sure that if your xps lib depends on libTree, you link it with libTree.

Cheers, Fons.

cstrato · May 16, 2010, 3:22pm

Dear Fons,

Thank you, however it turns out that in order to use the new Makefile.arch I need to change my Makefile from:

ifeq ($(PLATFORM),macosx)
		$(LD) $(SOFLAGS) $^ $(GLIBS) $(MYLIBS) $(OutPutOpt) $@ 
ifeq ($(MACOSX_MINOR),4)
		ln -sf $@ $(subst .$(DllSuf),.so,$@)
else
		$(LD) -bundle -undefined $(UNDEFOPT) $(LDFLAGS) $^ \
		   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)
endif

to:

ifeq ($(PLATFORM),macosx)
		$(LD) $(SOFLAGS)$@ $(LDFLAGS) $^ $(GLIBS) $(MYLIBS) $(OutPutOpt) $@
ifneq ($(subst $(MACOSX_MINOR),,1234),1234)
ifeq ($(MACOSX_MINOR),4)
		ln -sf $@ $(subst .$(DllSuf),.so,$@)
else
		$(LD) -bundle -undefined $(UNDEFOPT) $(LDFLAGS) $^ \
		   $(OutPutOpt) $(subst .$(DllSuf),.so,$@)
endif
endif

although it is not quite clear to me why I needed to change the first part.

Best regards
Christian

rdm · May 16, 2010, 11:03pm

Hi Christian,

this change was needed due to some refactoring and now LDFLAGS are needed.

ifneq ($(subst $(MACOSX_MINOR),,1234),1234) ifeq ($(MACOSX_MINOR),4) ln -sf $@ $(subst .$(DllSuf),.so,$@) else $(LD) -bundle -undefined $(UNDEFOPT) $(LDFLAGS) $^ \ $(OutPutOpt) $(subst .$(DllSuf),.so,$@) endif endif
is needed because on >= 10.5 there is no need anymore for separate .so and .dylib’s, just .so’s will do do.

Cheers, Fons.

cstrato · May 17, 2010, 6:06pm

Dear Fons,

Thank you for your explanation.

Best regards
Christian